Pysam

==============

This release implements further functionality in the VariantFile API
and includes several bugfixes:

* treat special case -c option in samtools view outputs to stdout even
if -o given, fixes 315
* permit reading BAM files with CSI index, closes 370
* raise Error if query name exceeds maximum length, fixes 373
* new method to compute hash value for AlignedSegment
* AlignmentFile, VariantFile and TabixFile all inherit from HTSFile
* Avoid segfault by detecting out of range reference_id and
next_reference in AlignedSegment.tostring
* Issue 355: Implement streams using file descriptors for VariantFile
* upgrade to htslib 1.3.2
* fix compilation with musl libc
* Issue 316, 360: Rename all Cython modules to have lib as a prefix
* Issue 332, hardclipped bases in cigar included by
pysam.AlignedSegment.infer_query_length()
* Added support for Python 3.6 filename encoding protocol
* Issue 371, fix incorrect parsing of scalar INFO and FORMAT fields in VariantRecord
* Issue 331, fix failure in VariantFile.reset() method
* Issue 314, add VariantHeader.new_record(), VariantFile.new_record() and
VariantRecord.copy() methods to create new VariantRecord objects
* Added VariantRecordFilter.add() method to allow setting new VariantRecord filters
* Preliminary (potentially unsafe) support for removing and altering header metadata
* Many minor fixes and improvements to VariantFile and related objects

Please note that all internal cython extensions now have a lib prefix
to facilitate linking against pysam extension modules. Any user cython
extensions using cimport to import pysam definitions will need
changes, for example::

cimport pysam.csamtools

will become::

cimport pysam.libcsamtools

=============

This is a bugfix release addressing some installation problems
in pysam 0.9.0, in particular:

* patch included htslib to work with older libcurl versions, fixes 262.
* do not require cython for python 3 install, fixes 260
* FastaFile does not accept filepath_index any more, see 270
* add AlignedSegment.get_cigar_stats method.
* py3 bugfix in VariantFile.subset_samples, fixes 272
* add missing sysconfig import, fixes 278
* do not redirect stdout, but instead write to a separately
created file. This should resolve issues when pysam is used
in notebooks or other environments that redirect stdout.
* wrap htslib-1.3.1, samtools-1.3.1 and bcftools-1.3.1
* use bgzf throughout instead of gzip
* allow specifying a fasta reference for CRAM file when opening
for both read and write, fixes 280

=============

Overview
--------

The 0.9.0 release upgrades htslib to htslib 1.3 and numerous other
enhancements and bugfixes. See below for a detailed list.

=============

This release contains numerous bugfixes and a first implementation of
a pythonic interface to VCF/BCF files. Note that this code is still
incomplete and preliminary, but does offer a nearly complete immutable
Pythonic interface to VCF/BCF metadata and data with reading and
writing capability.

=============

* samtools command now accept the "catch_stdout" option.

* get_aligned_pairs now works for soft-clipped reads.

* query_position is now None when a PileupRead is not aligned
to a particular position.

* AlignedSegments are now comparable and hashable.

===============

* Installation bugfix release.